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Please use this identifier to cite or link to this item: http://hdl.handle.net/11019/336

Title: InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation
Authors: Breuer, Karin
Foroushani, Amir K.
Laird, Matthew R
Chen, Carol
Sribnaia, Anastasia
Lo, Raymond
Winsor, Geoffrey L.
Hancock, Robert E. W.
Brinkman, Fiona S. L.
Lynn, David J
Keywords: InnateDB
Gene-expression
Mammalian innate immunity
Network visualization
Proteomics Standards Initiative Common Query Interface
Cellular systems
Issue Date: 24-Nov-2012
Publisher: Oxford University Press
Citation: Karin Breuer, Amir K. Foroushani, Matthew R. Laird, Carol Chen, Anastasia Sribnaia, Raymond Lo, Geoffrey L. Winsor, Robert E. W. Hancock, Fiona S. L. Brinkman, and David J. Lynn. InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation. Nucl. Acids Res. (2013) 41(D1): D1228-D1233 doi:10.1093/nar/gks1147
Series/Report no.: Nucleic Acids Research;vol 41
Abstract: InnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism.
Description: peer-reviewed
URI: http://hdl.handle.net/11019/336
http://dx.doi.org/10.1093/nar/gks1147
ISSN: 0305-1048
Appears in Collections:Animal & Bioscience

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